Unpack models archive to the directory with Doom3D source port (this was 'e:\games\doom' in my example).

Start 'Doom3DSetup.exe' to start Doom3D configuration utility. I had to adjust the 'Heap size' to '80' here, because the game didn't start complaining on the small size of the heap. I didn't notice any negative impact on perfomance though.

Click 'Advanced' to open Advanced Settings. Set the name of your md2 ini file ('Md2.ini') and set 'NoMD2Weapons' to '0' if you want to see the md2 replacements for the weapons in the game.

Click 'OK' to return to main window and select 'Run+Save' to start the game.